Neutron diffraction studies on aqueous solutions of glucose

Ion-Pairing Propensity in Guanidinium Salts Dictates Their Protein (De)stabilization Behavior

Since the proposition of the Hofmeister series, guanidinium (Gdm) salts hold a special mention in protein science owing to their contrasting effect on protein(s) depending on the counteranion(s). For example, while GdmCl is known to act as a potential protein denaturant, Gdm2SO4 offers minimal effect on protein structure. Despite the fact that theoretical studies reckon the formation of ion-pairing to be responsible for such behavior, experimental validation of this hypothesis is still in sparse. In this study, we combine electrochemical impedance spectroscopy (EIS) and THz spectroscopy to underline the effect of GdmCl and Gdm2SO4 on a model amide molecule N-methylacetamide (NMA). Molecular dynamics (MD) simulation studies predict that Gdm2SO4 forms heteroion pairing in water, which inhibits Gdm+ ions to approach NMA molecules, while in case of GdmCl, Gdm+ ions directly interact with NMA. The experimental findings on ion hydration, specifically the detailed analysis of the ion-water rattling mode, which appears in the THz frequency domain, unambiguously endorse this hypothesis. Our study establishes the fact that the propensity of ion-pairing in Gdm salts dictates their (de)stabilization effect on proteins.

Nanoconfinement's Dramatic Impact on Proton Exchange between Glucose and Water

Glucose nanoconfined by solubilization in water-containing AOT (sodium bis(2-ethylhexyl) sulfosuccinate) reverse micelles has been investigated using ¹H NMR. NMR spectra reveal well-defined signals for the glucose hydroxyl groups that suggest slow chemical exchange between them and the water hydroxyl groups. Using the EXSY (ZZ-exchange) method, the chemical exchange rate from water to glucose hydroxyl groups was measured for glucose in reverse micelles as a function of size (water pool diameter of ∼1-5 nm) at 25 °C. The chemical exchange rates observed in the nanoconfined interior are dramatically slower (5-20 times) than those observed for glucose in bulk aqueous solution at the same concentration as the micelle interior. Exchange rate constants are calculated via a mechanism that accounts for these observations, and implications of these results are presented and discussed.

Exploring Ion-Ion Interactions in Aqueous Solutions by a Combination of Molecular Dynamics and Neutron Scattering

Recent advances in computational and experimental techniques have allowed for accurate description of ion pairing in aqueous solutions. Free energy methods based on ab initio molecular dynamics, as well as on force fields accounting effectively for electronic polarization, can provide quantitative information about the structures and occurrences of individual types of ion pairs. When properly benchmarked against electronic structure calculations for model systems and against structural experiments, in particular neutron scattering, such force field simulations represent a powerful tool for elucidating interactions of salt ions in complex biological aqueous environments.

Glucose-Promoted Localization Dynamics of Excess Electrons in Aqueous Glucose Solution Revealed by Ab Initio Molecular Dynamics Simulation

Ab initio molecular dynamics simulations reveal that an excess electron (EE) can be more efficiently localized as a cavity-shaped state in aqueous glucose solution (AGS) than in water. Compared with that (∼1.5 ps) in water, the localization time is shortened by ∼0.7-1.2 ps in three AGSs (0.56, 1.12, and 2.87 M). Although the radii of gyration of the solvated EEs are all close to 2.6 Å in the four solutions, the solvated EE cavities in the AGSs become more compact and can localize ∼80% of an EE, which is considerably larger than that (∼40-60% and occasionally ∼80%) in water. These observations are attributed to a modification of the hydrogen-bonded network by the introduction of glucose molecules into water. The water acts as a promoter and stabilizer, by forming voids around glucose molecules and, in this fashion, favoring the localization of an EE with high efficiency. This study provides important information about EEs in physiological AGSs and suggests a new strategy to efficiently localize an EE in a stable cavity for further exploration of biological function.

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator

A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute-water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins.

Molecular level insight into intra-solvent interaction effects on protein stability and aggregation

Protein based therapeutics hold great promise in the treatment of human diseases and disorders and subsequently, they have become the fastest growing sector of new drugs being developed. Proteins are, however, inherently unstable and the degraded form can be quite harmful if administered to a patient. Of the various degradation pathways, aggregation is one of the most common and a cause for great concern. Aggregation suppressing additives have long been used to stabilize proteins, and they still remain the most viable option for combating this problem. Much work has been devoted toward investigating the behavior of commonly used additives and the resulting models give valuable insight toward explaining aggregation suppression. In a few cases, an explanation for unique behavior is lacking or new insight provides an alternate explanation. Additive selection and the development of better performing additives may benefit from a more refined understanding of how commonly used additives inhibit or enhance aggregation. In this review, we focus on recent molecular-level studies into how a select group of commonly used additives interact with proteins and subsequently influence aggregation. The intent of the review is not meant to be comprehensive for each additive but rather to provide new insights into additive-additive interactions, which may be contributing to protein-additive interactions. This is something that is often overlooked but yet essential to understanding the effect of additives on aggregation. The importance of understanding such interactions is clear when one considers that most formulations contain a mixture of cosolutes and that ideal stability might be better achieved through tuning intra-solvent interactions. We give an example of this when we describe how novel aggregation suppressing additives were developed from the knowledge gained from the reviewed studies.

Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments

Several laboratories have carried out molecular dynamics (MD) simulations of arginine interactions with lipid bilayers and found that the energetic cost of placing arginine in lipid bilayers is an order of magnitude greater than observed in molecular biology experiments in which Arg-containing transmembrane helices are inserted across the endoplasmic reticulum membrane by the Sec61 translocon. We attempt here to reconcile the results of the two approaches. We first present MD simulations of guanidinium groups alone in lipid bilayers, and then, to mimic the molecular biology experiments, we present simulations of hydrophobic helices containing single Arg residues at different positions along the helix. We discuss the simulation results in the context of molecular biology results and show that the energetic discrepancy is reduced, but not eliminated, by considering free energy differences between Arg at the interface and at the center of the model helices. The reduction occurs because Arg snorkeling to the interface prevents Arg from residing in the bilayer center where the energetic cost of desolvation is highest. We then show that the problem with MD simulations is that they measure water-to-bilayer free energies, whereas the molecular biology experiments measure the energetics of partitioning from translocon to bilayer, which raises the fundamental question of the relationship between water-to-bilayer and water-to-translocon partitioning. We present two thermodynamic scenarios as a foundation for reconciliation of the simulation and molecular biology results. The simplest scenario is that translocon-to-bilayer partitioning is independent of water-to-bilayer partitioning; there is no thermodynamic cycle connecting the two paths.

Simulation and Neutron Diffraction Studies of Small Biomolecules in Water

Modern biophysics has benefited greatly from the use of X-ray and neutron diffraction from ordered single crystals of proteins and other macromolecules to give highly detailed pictures of these molecules in the solid state. However, the most biologically relevant environments for these molecules are liquid solutions, and their liquid state properties are sensitive to details of the liquid structuring. The best experimental method for studying such structuring is also neutron diffraction, but of course, the inherent disorder of the liquid state means that these experiments cannot hope to achieve the level of informational detail available from single crystal diffraction. Nonetheless, recent advances in neutron beam intensity, beam stability, and detector sensitivity mean that it should be possible, at least in principle, to use such measurements to extract information about structuring in much more complex systems than have previously been studied. We describe a series of neutron diffraction studies of isotopically labeled molecules in aqueous solution which, when combined with results from computer simulations, can be used to extract conformational information of the hydration of the molecules themselves, essentially opening up new avenues of investigation in structural biology.

Additive empirical force field for hexopyranose monosaccharides

We present an all-atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all-atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the alpha- and beta-anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas-phase and condensed-phase properties of small-molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides, and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute-water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc-pVTZ//MP2/6-31G(d) level of theory. Although not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well-reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids.

Nanometer-scale ion aggregates in aqueous electrolyte solutions: guanidinium carbonate

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to characterize the structure of aqueous guanidinium carbonate (Gdm2CO3) solutions. The MD simulations found very strong hetero-ion pairing in Gdm2CO3 solution and were used to determine the best structural experiment to demonstrate this ion pairing. The NDIS experiments confirm the most significant feature of the MD simulation, which is the existence of strong hetero-ion pairing between the Gdm+ and CO3(2-) ions. The neutron structural data also support the most interesting feature of the MD simulation, that the hetero-ion pairing is sufficiently strong as to lead to nanometer-scale aggregation of the ions. The presence of such clustering on the nanometer length scale was then confirmed using small-angle neutron scattering experiments. Taken together, the experiment and simulation suggest a molecular-level explanation for the contrasting denaturant properties of guanidinium salts in solution.

X-ray and neutron scattering studies of the hydration structure of alkali ions in concentrated aqueous solutions

The presence of ions in water provides a rich and varied environment in which many natural processes occur with important consequences in biology, geology and chemistry. This article will focus on the structural properties of ions in water and it will be shown how the 'difference' methods of neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction (AXD) can be used to obtain direct information regarding the radial pair distribution functions of many cations and anions in solution. This information can subsequently be used to calculate coordination numbers and to determine ion-water conformation in great detail. As well as enabling comparisons to be made amongst ions in particular groups in the periodic table, such information can also be contrasted with results provided by molecular dynamics (MD) simulation techniques. To illustrate the power of these 'difference' methods, reference will be made to the alkali group of ions, all of which have been successfully investigated by the above methods, with the exception of the radioactive element francium. Additional comments will be made on how NDIS measurements are currently being combined with MD simulations to determine the structure around complex ions and molecules, many of which are common in biological systems.

The Structure of Aqueous Guanidinium Chloride Solutions

The combination of neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations to characterize the structuring in an aqueous solution of the denaturant guanidinium chloride is described. The simulations and experiments were carried out at a concentration of 3 m at room temperature, allowing for an examination of any propensity for ion association in a realistic solution environment. The simulations satisfactorily reproduced the principal features of the neutron scattering and indicate a bimodal hydration of the guanidinium ions, with the N-H groups making well-ordered hydrogen bonds in the molecular plane, but with the planar faces relatively deficient in interactions with water. The most striking feature of these solutions is the rich ion-ion ordering observed around the guanidinium ion in the simulations. The marked tendency of the guanidinium ions to stack parallel to their water-deficient surfaces indicates that the efficiency of this ion as a denaturant is due to its ability to simultaneously interact favorably with both water and hydrophobic side chains of proteins.

Molecular dynamics of glucose in solution: A quasielastic neutron scattering study

The molecular dynamics of glucose dissolved in heavy water have been investigated at 280 K by the technique of quasielastic neutron scattering. The scattering was described by a dynamic structure factor that accounts for decoupled diffusive jumps and free rotational motions of the glucose molecules. With increasing glucose concentration, the diffusion constant decreases by a factor five and the time between jumps increases considerably. Our observations validate theoretical predictions concerning the impact of concentration on the environment of a glucose molecule and the formation of cages made by neighboring glucose molecules at higher concentrations.